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capsid_portal_protein

Euk-Vir

Saimiriine_betaherpesvirus_4

capsid_portal_protein__YP_004940265__Saimiriine_betaherpesvirus_4__1535247

Identity

Accession:: YP_004940265 ↗
Protein ID:: capsid_portal_protein
Kingdom:: euk

Quality

75.0 mean pLDDT

Taxonomy

Heunggongvirae› Peploviricota› Herviviricetes› Herpesvirales› Orthoherpesviridae› Cytomegalovirus› Saimiriine_betaherpesvirus_4

TaxID: 1535247

Cluster

View cluster (76 members)

3D Structure

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Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 medium residues 90-127_570-615

PDB

Domain cluster: rep: Structural_protein__YP_214104__Murid_betaherpesvirus_1__10366__D92-124_566-612

CATH (20)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
4okvE00	6.10.140.1890	Special › Helix non-globular › Helix Hairpins ›	0.89	34.0	3.92e-01	90.5%	49.2%
7p3rA01	1.20.1170.10	Mainly Alpha › Up-down Bundle › Hemolysin E; Chain: A; ›	0.81	40.0	2.64e-01	100.0%	12.6%
7dluA01	1.10.287.1260	Mainly Alpha › Orthogonal Bundle › Helix Hairpins ›	0.79	38.0	3.48e-01	96.4%	37.1%
2xokP00	1.20.20.10	Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C	0.75	37.0	4.00e-01	100.0%	54.1%
2fb5A01	1.10.287.770	Mainly Alpha › Orthogonal Bundle › Helix Hairpins › YojJ-like	0.75	34.0	3.73e-01	94.0%	51.4%
2dw4A03	1.10.287.80	Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ATP synthase, gamma subunit, helix hairpin domain	0.73	38.0	3.56e-01	100.0%	42.6%
4kp3C00	1.20.58.1770	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 ›	0.60	39.0	4.04e-01	98.8%	70.4%
4lwsA00	1.10.287.1060	Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like	0.59	33.0	3.19e-01	100.0%	44.0%
4zvaA00	1.10.490.10	Mainly Alpha › Orthogonal Bundle › Globin-like › Globins	0.56	41.0	3.43e-01	78.6%	87.2%
3a7mA01	1.20.58.380	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Flagellar protein flit.	0.56	48.0	4.46e-01	97.6%	85.5%
3rrkA02	1.20.1460.20	Mainly Alpha › Up-down Bundle › subunit c (vma5p) of the yeast v-atpase, domain 2 ›	0.54	39.0	3.22e-01	76.2%	77.4%
2lm9A00	1.20.58.970	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 ›	0.54	41.0	3.96e-01	79.8%	100.0%
7s0rB01	1.20.81.20	Mainly Alpha › Up-down Bundle › Receptor-associated Protein ›	0.53	43.0	4.52e-01	89.3%	100.0%
3ph0C00	1.25.40.1040	Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat ›	0.52	32.0	3.93e-01	78.6%	100.0%
1mhyG02	1.20.1280.30	Mainly Alpha › Up-down Bundle › Monooxygenase › Methane monooxygenase, gamma chain, domain 2	0.52	41.0	4.34e-01	88.1%	100.0%
1x4pA00	1.10.10.790	Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Surp module	0.52	36.0	3.92e-01	76.2%	90.9%
3q23A08	1.20.140.110	Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 ›	0.52	38.0	3.08e-01	76.2%	92.9%
4mycA01	1.20.1560.10	Mainly Alpha › Up-down Bundle › ABC transporter transmembrane region fold › ABC transporter type 1, transmembrane domain	0.51	40.0	2.80e-01	88.1%	82.3%
2wy4A00	1.10.490.10	Mainly Alpha › Orthogonal Bundle › Globin-like › Globins	0.51	39.0	3.41e-01	84.5%	98.6%
2pihA00	1.20.1500.10	Mainly Alpha › Up-down Bundle › YheA-like fold › YheA/YmcA-like	0.51	38.0	3.33e-01	77.4%	70.7%

ECOD (24)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
4937584	5058.1.1.0 ↗	alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region	0.83	35.0	3.69e-01	91.7%	45.3%
3362279	2006.1.4.0 ↗	a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like	0.80	41.0	4.21e-01	100.0%	52.5%
4050521	547.1.1.1 ↗	alpha duplicates or obligate multimers › Glutamyl tRNA-reductase dimerization domain › Glutamyl tRNA-reductase dimerization domain › Glutamyl tRNA-reductase dimerization domain › GlutR_dimer	0.78	40.0	3.70e-01	100.0%	40.8%
3788874	148.1.1.18 ↗	alpha arrays › Histone-like › Histone-related › Histone › CENP-S	0.76	37.0	3.37e-01	96.4%	35.5%
4982777	3291.1.1.238 ↗	alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › DUF7121	0.76	40.0	2.87e-01	100.0%	18.7%
4029754	605.1.1.0 ↗	alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase	0.76	38.0	3.86e-01	100.0%	48.2%
3640760	3291.1.1.17 ↗	alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › DUF202	0.75	36.0	3.23e-01	95.2%	34.5%
3575774	604.39.1.0 ↗	alpha bundles › Spectrin repeat-like › S-component of energy-coupling factor (ECF) transporters › S-component of energy-coupling factor (ECF) transporters	0.74	39.0	3.29e-01	100.0%	31.4%
3611166	3755.3.1.0 ↗	alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin	0.73	39.0	2.91e-01	100.0%	22.0%
3727274	3758.1.1.69 ↗	alpha bundles › Bacterial hemolysins-like › Bacterial hemolysins › Bacterial hemolysins › PF30554	0.73	39.0	2.76e-01	100.0%	18.3%
5018642	5058.1.1.2 ↗	alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › MS_channel_1st	0.71	38.0	3.55e-01	88.1%	42.9%
4089827	192.1.1.34 ↗	alpha bundles › Long alpha-hairpin › GreA transcript cleavage protein, N-terminal domain › GreA transcript cleavage protein, N-terminal domain › DUF444	0.70	36.0	3.82e-01	98.8%	54.7%
2832654	5058.1.1.1 ↗	alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › MS_channel_1st_1,MS_channel_1st	0.68	34.0	3.32e-01	96.4%	41.5%
3643902	5086.1.1.0 ↗	alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins	0.68	37.0	3.14e-01	100.0%	34.6%
5024787	7064.1.1.0 ↗	alpha bundles › Transmembrane domain of VIT1 › Transmembrane domain of VIT1 › Transmembrane domain of VIT1	0.68	35.0	2.88e-01	98.8%	27.3%
4378877	3711.1.1.20 ↗	alpha bundles › LTXXQ motif family protein › LTXXQ motif family protein › LTXXQ motif family protein › DUF444	0.68	35.0	3.73e-01	100.0%	54.7%
3191997	5041.1.1.15 ↗	extended segments › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › Tmemb_170	0.56	44.0	4.04e-01	84.5%	100.0%
4446713	604.11.1.1 ↗	alpha bundles › Spectrin repeat-like › XseB-like › XseB-like › Exonuc_VII_S	0.54	42.0	4.39e-01	86.9%	92.0%
5030095	192.4.1.0 ↗	alpha bundles › Long alpha-hairpin › Ribosomal protein L29 (L29p) › Ribosomal protein L29 (L29p)	0.52	42.0	4.44e-01	88.1%	96.0%
3781350	5041.1.1.20 ↗	extended segments › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › PF26669	0.52	38.0	3.35e-01	100.0%	53.3%
3419377	1075.4.1.1 ↗	alpha bundles › Type II ABC exporter transmembrane domain fold › Type I ABC exporter transmembrane domain fold › Type I ABC exporter transmembrane domain fold › ABC_membrane	0.52	39.0	3.08e-01	84.5%	73.9%
5072135	2498.1.1.10 ↗	mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › Peptidase_M48	0.51	45.0	3.44e-01	97.6%	44.1%
3797019	219.1.1.0 ↗	a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases	0.51	37.0	2.53e-01	76.2%	29.3%
3240670	5001.1.1.35 ↗	alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7TM_GPCR_Srsx	0.50	42.0	3.02e-01	98.8%	42.1%

D2 medium residues 128-281

PDB

Domain cluster: rep: JM72__YP_238375__Macaca_fuscata_rhadinovirus__272551__D50-239

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF01763.23 best	Herpes_UL6	92.0	4.50e-26	99.4%	26.1%

CATH (5)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
1w0bA01	1.20.58.420	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › AHSP	0.59	36.0	4.39e-01	81.8%	100.0%
3rmiA00	1.20.59.10	Mainly Alpha › Up-down Bundle › Chorismate Mutase Domain, subunit A › Chorismate mutase	0.56	38.0	4.40e-01	75.3%	100.0%
8ek4A01	1.20.120.20	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Apolipoprotein	0.55	39.0	4.13e-01	70.8%	100.0%
1q6aA00	1.10.1240.30	Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › KaiA/RbsU domain	0.53	31.0	3.56e-01	72.1%	80.4%
4kb2A01	1.10.132.20	Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor	0.50	35.0	4.05e-01	76.6%	100.0%

ECOD (11)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3845878	621.1.1.0 ↗	alpha bundles › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain	0.69	35.0	4.83e-01	79.2%	100.0%
4599106	604.9.1.1 ↗	alpha bundles › Spectrin repeat-like › Ribosomal protein S20 › Ribosomal protein S20 › Ribosomal_S20p	0.67	38.0	4.83e-01	70.1%	95.6%
3259377	621.1.1.0 ↗	alpha bundles › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain	0.63	39.0	4.77e-01	80.5%	100.0%
4092432	101.11.1.1 ↗	alpha arrays › HTH › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 › PNPase	0.60	35.0	4.44e-01	70.1%	94.7%
3596026	310.2.1.0 ↗	a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF	0.58	41.0	4.22e-01	72.1%	98.0%
3919099	621.1.1.8 ↗	alpha bundles › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › GVIN1	0.58	44.0	4.74e-01	79.2%	92.6%
3584182	604.9.1.18 ↗	alpha bundles › Spectrin repeat-like › Ribosomal protein S20 › Ribosomal protein S20 › Zip	0.57	32.0	4.11e-01	77.3%	98.8%
3743731	3615.1.1.0 ↗	alpha bundles › Bacterial dynamin-like protein helical domain › Bacterial dynamin-like protein helical domain › Bacterial dynamin-like protein helical domain	0.52	39.0	3.49e-01	76.0%	64.8%
3927052	319.1.1.3 ↗	beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones › CS	0.52	22.0	2.58e-01	72.7%	51.3%
5029796	192.2.1.0 ↗	alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin	0.51	27.0	3.00e-01	90.3%	64.2%
3614576	109.4.1.0 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat	0.50	43.0	3.20e-01	91.6%	55.4%

D3 medium residues 316-379_498-521

PDB